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Body colors are an important trait for the survival and reproduction of animals. In this study, transcriptomes and related single nucleotide polymorphisms (SNPs) of black- and red-colored Plectropomus leopardus (Lacépède) were identified to investigate important molecules and SNP markers associated with body color formation. In the comparison of red- and black-colored groups, 489 differential expressed genes (DEGs) were detected and among them, 236 up- and 253 down-regulated genes were found in the red-colored group. Gene ontology (GO) analysis of DEGs showed that pigmentation associated terms including pigment granule, pigmentation, melanin metabolic process, tyrosine metabolic process, pigment metabolic process, and pigmentation cell differentiation were enriched. Kyoto encyclopedia of genes and genomes (KEGG) analysis of DEGs presented that melanin related pathways (tyrosine metabolism and melanogenesis) were enriched. Furthermore, lipid metabolism and immune-related metabolism were also enriched. A total of 1,048,575 SNPs were detected from the transcriptome, and among them, 627,172 SNPs were located in the gene region. A total of 1323 SNPs were identified as differential SNPs in the comparison of black- and red-colored groups and were located in 1127 genes. Among the 1127 genes, 20 genes were identified as DEGs and were comprised of 9 SNPs with a potential role in body color selective breeding in fish farming.

Biomineralization-controlled exo-/endoskeleton growth contributes to body growth and body size diversity. Molluscan shells undergo ectopic biomineralization to form the exoskeleton and biocalcified "pearl" involved in invading defence. Notably, exo-/endoskeletons have a common ancestral origin, but their regulation and body growth are largely unknown. This study employed the pearl oyster, Pinctada fucata marntensii, a widely used experimental model for biomineralization in invertebrates, to perform whole-genome resequencing of 878 individuals from wild and breeding populations. This study characterized the genetic architecture of biomineralization-controlled growth and ectopic biomineralization. The insulin-like growth factor (IGF) endocrine signal interacted with ancient single-copy transcription factors to form the regulatory network. Moreover, the "cross-phylum" regulation of key long noncoding RNA (lncRNA) in bivalves and mammals indicated the conserved genetic and epigenetic regulation in exo-/endoskeleton growth. Thyroid hormone signal and apoptosis regulation in pearl oysters affected ectopic biomineralization in pearl oyster. These findings provide insights into the mechanism underlying the evolution and regulation of biomineralization in exo-/endoskeleton animals and ectopic biomineralization.

Postoperative care is a critical step of pearl culture that ultimately determines culture success. To determine the effect of dietary vitamin D3 (VD3) levels on immunity and antioxidant capacity of pearl oyster Pinctada fucata martensii during postoperative care and explore the mechanisms behind this phenomenon, five isonitrogenous and isolipidic experimental diets were formulated by adding different levels of dietary VD3 (0, 500, 1000, 3000, and 10000 IU/kg), and the diets were fed to five experimental groups (EG1, EG2, EG3, EG4, and EG5) in turn and cultured indoors. The control group (CG) was cultured in the natural sea. Pearl oysters that were 1.5 years old were subjected to nucleus insertion. After culturing for 30 days, EG3 exhibited significantly higher survival rates than those in CG and EG5 (P 0.05). Moreover, EG3 exhibited the highest activities of alkaline phosphatase, acid phosphatase, catalase, superoxide dismutase, and lysozyme. However, EG5 achieved the highest activities of glutathione peroxidase. Metabolomics-based profiling of pearl oysters fed with high levels of dietary VD3 (EG5) and optimum levels of dietary VD3 (EG3) revealed 76 significantly differential metabolites (SDMs) (VIP 1 and P 0.05). Pathway analysis indicated that SDMs were involved in 21 pathways. Furthermore, integrated key metabolic pathway analysis suggested that pearl oysters in EG5 regulated the pentose phosphate pathway, glutathione metabolism, sphingolipid metabolism, and arachidonic acid metabolism in response to stress generated from excessive VD3. These findings had significant implications on strengthening the future development and application of VD3 in aquaculture of pearl oyster P. f. martensii.

The effects of astaxanthin on growth performance, digestive enzyme activity, antioxidant capacity, immune ability, resistance to Vibrio harveyi infection of coral trout (Plectropomus leopardus, initial weight 17.44 ± 0.05 g) were studied by 8-week feeding trial. Four iso-nitrogenous and iso-lipidic experimental diets containing astaxanthin 0 (A0), 0.05 (A1), 0.1 (A2) and 0.2 (A3) g/kg were formulated with the addition of Haematococcus pluvialis powder (astaxanthin content accounts for 100 g/kg) of 0, 0.5, 1.0 and 2.0 g/kg, separately. The feeding experiment lasted for 56 days, and it was found that supplementing the diet with astaxanthin-rich H. pluvialis powder had no significant impact on the growth performance about coral trout (P 0.05). Compared with the A0 group, the activities of amylase, lipase, and trypsin in the liver of the A2 group was dramatically increased (P 0.05); catalase (CAT), superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px) activities and total antioxidant capacity (T-AOC) level in serum and liver were dramatically higher in the A2 group before as well as after the challenge (P 0.05); after the challenge, the acid phosphatase (ACP) and lysozyme (LZ) activities, and complement (C3 and C4) contents in serum and liver were significantly raised for the A2 group (P 0.05); the liver relative expressions of copper-zinc superoxide dismutase (sod-1), manganese superoxide dismutase (sod-2), cat, acp6, akp, lz-c, immunoglobulin M (igm), c3, and c4-b in the A2 group were significantly up-regulated before and after the challenge (P 0.05); the rate of survival follow V. harveyi challenge in the group A2 was dramatically higher (P 0.05). In summary, this study indicated that adding 1.0 g/kg astaxanthin-rich H. pluvialis powder (the content of astaxanthin is 0.091 g/kg) could improve the digestive enzyme activity, antioxidant capacity, immunity, and the ability to resist the challenge of V. harveyi in coral trout.

Environmental factors, including antibiotics such as tetracycline, can alter biological processes in plants. To ascertain how cell/tissue response to tetracycline, a multi-omic analysis was implemented to explore the molecular mechanism of tetracycline influencing the growth of ryegrass root. Tetracycline induced extensive changes in the root metabolome in plants, particularly impacting metabolites of flavonoid metabolic pathways, which were supported through consistent differences between transcriptome and proteome. Cross-comparison between mRNA and protein contents considered the authentication of congruence with related metabolites and revealed changes of several biological processes under tetracycline stress. Overall, we present an undemanding multi-omic strategy to survey the significant influence on the root under tetracycline stress.

Background Marine bivalves undergo complex development processes, such as shell morphology conversion and changes of anatomy and life habits. In this study, the transcriptomes of pearl oyster Pinctada fucata martensii and Pacific oyster Crassostrea gigas at different development stages were analyzed to determine the key molecular events related to shell formation, settlement and metamorphosis. Result According to the shell matrix proteome, biomineralization-related genes exhibited a consensus expression model with the critical stages of shell formation. Differential expression analysis of P. f. martensii, revealed the negative regulation and feedback of extracellular matrixs as well as growth factor pathways involved in shell formation of larvae, similar to that in C. gigas. Furthermore, neuroendocrine pathways in hormone receptors, neurotransmitters and neuropeptide receptors were involved in shell formation, settlement and metamorphosis. Conclusion Our research demonstrated the main clusters of regulation elements related to shell formation, settlement and metamorphosis. The regulation of shell formation and metamorphosis could be coupled forming the neuroendocrine-biomineralization crosstalk in metamorphosis. These findings could provide new insights into the regulation in bivalve development. Electronic supplementary material The online version of this article (10.1186/s12864-019-5505-8) contains supplementary material, which is available to authorized users.

Keratan sulfate possesses considerable amounts of negatively charged sulfonic acid groups and participates in biomineralization. In the present study, we investigated characteristics and functions of a CHST1 gene identified from the pearl oyster Pinctada fucata martensii (PmCHST1b) which participated in the synthesis of keratan sulfate. PmCHST1b amino acid sequence carried a typical sulfotransferase-3 domain (sulfotransfer-3 domain) and belonged to membrane-associated sulfotransferases. Homologous analysis of CHST1 from different species showed the conserved motif (5' PSB motif and 3' PB motif) which interacted with 3'-phosphoadenosine-5'-phosphosulfate (PAPS). Structure analysis of sulfotransferase domain indicted that PmCHST1b showed the conserved catalytic structure character and the relationships presented in the phylogenetic tree conformed to that of traditional taxonomy. Expression pattern of PmCHST1b in different tissues and development stages showed that PmCHST1b widely expressed in all the detected tissues and development stages and showed the highest expression level in the central zone of mantle (MC). PmCHST1b expressed highly in the trochophore, D-stage larvae and spat which corresponded to prodissoconch and dissoconch shell formation, respectively. RNA interference (RNAi) successfully inhibited expression level of PmCHST1b in MC (P

Understanding of nitrogen stable isotope variation in maize hybrids might help obtaining information on nitrogen absorption and distribution in different maize hybrids. In this study, we examined the nitrogen isotopic composition of different parts of maize hybrids under a laboratory culture experiment. The results showed that the δ15N values of different parts of the maize hybrid and its parents were ordered as follows: δ15Nstem>δ15Nleaf>δ15Nroot. The variation pattern of δ15N between the roots and leaves(Δδ15Nroot-leaf) of the maize hybrid was the same as that of δ15N between the roots and stems (Δδ15Nroot-stem). Therefore, the order of Δδ15Nroot-leaf as well as Δδ15Nroot-stem was as follows: Δδ15Nroot-leaf of the maize hybrid>Δδ15Nroot-leaf of the female parent (T4)>Δδ15Nroot-leaf of the male parent (803) and Δδ15Nroot-stem of the maize hybrid>Δδ15Nroot-stem of the female parent (T4)>Δδ15Nroot-stem of the male parent (803). This order is consistent with heterosis, indicating that differences in δ15N reflect the phenomenon of heterosis. The present study provides data in support of using the isotope technique to determine nitrogen distributions inside a plant and guide crossbreeding.

Fibroblast growth factor 18 (FGF18) plays an important functional role in skeletal growth and development. The FGF18 gene was characterized in pearl oyster Pinctada fucata martensii (PmFGF18) with the full-length sequence containing an open reading frame of 714 bp encoding 237 amino acids. The domain analysis of PmFGF18 showed a distinctive FGF domain, with a high similarity to FGF18 protein sequences from Crassostrea gigas (43.35%) and C. virginica (37.43%). PmFGF18 expression was revealed in all analyzed tissues with a significantly higher expression level in the fast-growing group than the slow-growing group. The analysis of PmFGF18 polymorphism demonstrated 33 SNPs (single nucleotide polymorphisms) in the CDS and promoter region of PmFGF18 sequence. Association analysis revealed 19 SNPs (2 SNPs from CDS and 17 SNPs from the promoter region) associating significantly with growth traits. Among the associated SNPs, one SNP g.50918198 A &gt, C was verified in the other breeding line. Therefore, PmFGF18 can be utilized as a candidate gene for growth, and its related SNPs could be used in selective breeding of P. f. martensii for the improvement of growth traits.

MicroRNAs (miRNAs) are endogenous small non-coding RNAs that regulate gene expression at the post-transcriptional level and play important roles in many biological processes, including controlling body color differentiation in many different animals. However, the mechanism by which specific miRNAs regulate body color formation in leopard coral groupers has remained largely elusive. In the present study, we sequenced the miRNAs of red and black skin samples from leopard coral grouper (Plectropomus leopardus) with the Illumina HiSeq X_Ten platform to explore the function of miRNAs in the body color formation. A total of 15.21 M and 13.69 M high quality reads were obtained from the black and red skin samples, respectively. Within these sequences, 626 known and 354 novel miRNAs were identified. When comparing across the two groups, we found 60 differentially expressed miRNAs, with red-colored group having 44 up-regulated miRNAs including miR-215, miR-2188, miR-194, miR-122, novel-m0118, and 16 down-regulated miRNAs including miR-187, novel-m0189, novel-m0145, compared with black-colored group (p 1). Integrated analysis of differentially expressed miRNAs and mRNAs identified 846 miRNA-mRNA pairs with opposite expression patterns. Go terms and KEGG pathway enrichment analyses showed that these putative target mRNAs were enriched for functions involving in endocrine systems, immune response, and lipid metabolism. The present study shows the potential role of miRNAs in the body color formation of fish and provides a molecular foundation to explain the role of epigenetics in fish body color selections.

Cyclin dependent kinase-7 (Cdk-7) is a protein kinase associated with regulating the cell cycle, cell differentiation and proliferation, apoptosis and inflammatory response. This study characterized the full cDNA sequence of Cdk-7 in Pinctada fucata martensii (PmCdk-7). A full length sequence of 1473bp with an open reading frame (ORF) of 915bp and encodes a 304aa, 5′-UTR of 58bp and a 3′-UTR of 500bp was obtained. The construed amino acid sequence of PmCdk-7 comprised of a Serine/Threonine protein kinases, catalytic (S_TKc) domain with a protein kinases ATP-binding region signature (14-38aa) and the serine/Threonine protein kinases active-site signature (129-141aa) within the domain. Tissue distribution analysis revealed a high relative mRNA expression of PmCdk-7 within haemocytes. Following the insertion operation (grafting), the relative expression levels of PmCdk-7 in the haemocyte was expressed differentially among the studied groups; the black shell colored selected line (BS) and the control group (CG). High expression was recorded between 12 h and 5d with a peak at 3d suggesting a heightened level of DNA replication and inflammatory response during the pearl-sac formation and this expression was higher in BS than CS showcasing, the heightened immune capacity of BS to grafting operation. Immune stimulation experiment with bacterial endotoxin and a viral mimic revealed PmCdk-7 response to pathogenic stress. The results from our study showed that PmCdk-7 performs a vital function during the cell cycle by aiding DNA replication and also aid response to inflammations generated due to the incision from the grafting operation and long exposure to immune-stimulants (pathogens).

The C1q-domain-containing (C1qDC) proteins are a family of proteins characterized by a globular C1q (gC1q) domain in their C-terminus which hold the potential function in the shell formation as shell matrix proteins. In this study, a C1qDC protein was identified and characterized in pearl oyster (Pinctada fucata martensii) (PmC1qDC) to explore its function in nacre formation. The PmC1qDC-deduced protein sequence carried a typical globular C1q (gC1q) domain that possessed the typical 10-stranded β-sandwich fold with a jelly-roll topology common to all C1qDC family members and shared high homology with other gC1q domains. Homologous analysis of PmC1qDC presented it contained conserved secondary structure and Phe135, Phe155, Tyr166, Phe173, Tyr181, Phe183, and Phe256 amino acid residues. Expression pattern analysis showed that PmC1qDC expressed in all the detected tissues and exhibited a significantly higher expression level in nacre formation-associated tissues. After the shell notching, the expression level of PmC1qDC showed significantly up-regulation after 12 h in the central zone of mantle (MC). PmC1qDC expression significantly decreased in the MC after RNA interference (RNAi). Furthermore, disordered crystals with evident rough surface and irregular crystal tablets were observed in the nacre after RNAi. Results suggested that PmC1qDC affects the shell nacre formation, which is significant to improve the pearl production of pearl oyster.

In this study, we developed microsatellite markers, analyzed their distribution and frequency and verified polymorphism based on the transcriptome data of pearl oyster Pinctada maxima. Totally, 58,121 potential EST-SSRs from 145,877 sequences were identified. We randomly selected 100 of these primer pairs for further validation in the stock, 76 primer pairs were successfully amplified and 25 primer pairs were found to be polymorphic. The number of alleles at each locus ranged from 2 to 5, with an average allele number of 2.96. The observed heterozygosity ranged from 0.185 to 0.931 with an average of 0.656. The expected heterozygosity ranged from 0.337 to 0.754 with an average of 0.552. The polymorphic information content ranged from 0.263 to 0.690 with an average of 0.462. These markers will provide an effective tool for genetic diversity, genetic map construction and molecular-assisted breeding in the species of P. maxima. Keywords: Pinctada maxima, SSR markers, Polymorphism, Genetic diversity

Similar to other marine bivalves, Pinctada maxima shows unsynchronized growth, but the underlying metabolic mechanisms have not been studied. In this study, gold-lipped pearl oyster P. maxima from cultured stocks were selected to produce progeny stock. At 180 days, the stock was sorted by size, and fast-growing individuals and slow-growing individuals were separately sampled. Then, a metabolomic approach based on gas chromatography–mass spectroscopy was applied to assess the metabolite changes between the fast-growing and slow-growing groups of P. maxima and to understand the mechanism of their unsynchronized growth. In the metabolomics assay, among the 896 peaks isolated, 111 metabolites were revealed a spectral similarity value of >700 by using mass spectrum matching, and 48 were considered as significantly different metabolites (SDMs; VIP > 1 and P

Natural disasters and environmental pollution are the main problems for traditional offshore culture. Pearl oyster culture through industrial farming can prevent these difficulties, but food availability is limited. In this study, we formulated two diets, P3 and P5, with yeast powder and corn gluten, respectively, as major protein sources. Two experimental groups (EG1 and EG2) were separately fed with P3 and P5 diets indoors. After 45 days of feeding, GC–TOF/MS-based metabolomics of the hepatopancreas was performed to assess the effect of different formulated diets on pearl oyster (Pinctada fucata martensii) combined with growth performance. EG1 displayed significantly faster absolute growth rate and higher survival rate than EG2. In the metabolomic assay, 125 metabolites were identified by mass spectrum matching with a spectral similarity value (SV) > 700, and 35 were considered significantly different metabolites (SDMs) (VIP > 1 and P 0.1). The impact values of phenylalanine, tyrosine, and tryptophan biosynthesis, ascorbate and aldarate metabolism, phenylalanine metabolism, inositol phosphate metabolism, tyrosine metabolism, sulfur metabolism, and cysteine and methionine metabolism were 0.500, 0.500, 0.308, 0.219, 0.207, 0.167, and 0.161, respectively. Further integrated key metabolic pathway analysis showed that EG2 exhibited lower capability for inositol phosphate metabolism, ascorbate and aldarate metabolism, phenylalanine metabolism, and tyrosine metabolism. This study suggested that yeast powder is a better protein source of formulated diet for pearl oysters than corn gluten.

Background: Molluscs can accumulate carotenoids in their body tissues by predominantly feeding on aquatic plant sources. Carotenoid transport and absorption are determined by the regulation of various proteins such as Scavenger receptor class B(SR-BI). We report the identification and characterisation of pearl oyster Pinctada fuctada martensii SR-BI (PmSR-BI). The correlation between total carotenoid content (TCC) and gene expression was also estimated. Results: The full-length cDNA of PmSR-BI was 1828 bp, including an open-reading frame encoding of 1518 bp with a pI value of 5.83. PmSR-BI protein contains a hydrophobic CD36 domain and four centrally clustered cysteine residues for the arrangement of disulphide bridges. The deduced amino acid sequence had an identity of 30% to 60% with the SR-B of other organisms. Reverse transcription polymerase chain reaction analysis showed that mRNA transcripts were expressed in multiple tissues of adult pearl oyster. A higher expression of PmSR-BI gene was observed in the hepatopancreas than in the adductor muscle, gill and mantle. The TCC and gene expression of PmSR-BI were significantly correlated (P

In this study, we formulated five diets, namely, P1, P2, P3, P4 and P5, with Chlorella sp. powder, Spirulina platensis powder, yeast powder, soybean meal and corn gluten, respectively, as major protein sources. A feeding experiment was designed to evaluate the effects of formulated diets on the growth performance, immunity and antioxidant and biomineralization capacity of juvenile pearl oyster (Pinctada fucata martensii). In the experiments, the five groups were separately fed with P1, P2, P3, P4 and P5 diets. After 45 days of feeding, pearl oysters fed on P1, P2, P3 and P4 diets showed significantly higher absolute growth rate and protease and amylase activities than those fed on P5 diet (P < 0.05). Moreover, pearl oysters fed on P1, P2, P3 and P4 diets exhibited significantly higher activities of alkaline phosphatase (AKP), superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPx) (P < 0.05). Significantly higher expression levels of SOD, GPx, CAT, heat shock protein (HSP) 70, HSP90, nacrein, pif177 and pearlin mRNA were observed in pearl oysters fed on P1, P2, P3 and P4 diets relative to those fed on P5 (P < 0.05). Results suggested the suitability of Chlorella sp. powder, S. platensis powder, yeast powder and soybean meal as protein sources for development of formulated diets for pearl oyster P. f. martensii.

Background : C4ST-1 catalyses the transfer of sulfate groups in the sulfonation of chondroitin during chondroitin sulfate synthesis. Chondroitin sulfate consists of numerous copies of negatively charged sulfonic acid groups that participate in the nucleation process of biomineralization. In the present study, we obtained two CHST11 genes ( PmCHST11a and PmCHST11b ) which encoded the C4ST-1 and explored the functions of these genes in the synthesis of chondroitin sulfate and in the formation of the nacreous layer of shells. Results: Both PmCHST11a and PmCHST11b had a sulfotransferase-2 domain, a signal peptide and a transmembrane domain. These properties indicated that these genes localise in the Golgi apparatus. Real-time PCR revealed that both PmCHST11a and PmCHST11b were highly expressed in the central zone of the mantle tissue. Inhibiting PmCHST11a and PmCHST11b via RNA interference significantly decreased the expression levels of these genes in the central zone of the mantle tissue and the concentration of chondroitin sulfate in extrapallial fluid. Moreover, shell nacre crystallised irregularly with a rough surface after RNA interference. Conclusions: This study indicated that PmCHST11a and PmCHST11b are involved in the nacre formation of P. fucata martensii through participating in the synthesis of chondroitin sulfate. Normal 0 false false false EN-US ZH-CN X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabla normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.5pt; mso-bidi-font-size:11.0pt; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi; mso-font-kerning:1.0pt; mso-fareast-language:ZH-CN;}

The pearl oyster, Pinctada fucata martensii, produces high-quality pearls. During pearl production, excess immune and inflammatory response after transplantation will lead to nucleus rejection, pearl sac formation failure, and death of the host pearl oyster. The hemocyte transcriptome and fatty acid (FA) contents in the adductor muscle before and after transplantation were analyzed to investigate the response of pearl oyster P. f. martensii to allograft-induced stress from lipid metabolism. The hemocyte transcriptome analysis detected 193 lipid metabolism-related genes, such as the elongation of very long-chain FA protein 5, acyl-CoA 6-desaturase, cytochrome P450, phospholipase A2, glycerol-3-phosphate O-acyltransferase, and prostaglandin-H2 d-isomerase. Pathway enrichment analyses revealed that these genes were mainly involved in the "biosynthesis of unsaturated FAs," "FA biosynthesis," "ARA metabolism," and "glycerolipid metabolism." An analysis of FA contents in the adductor muscle indicated no significant difference in the contents of lauric acid, myristic acid, pentadecanoic acid, palmitic acid, palmitoleic acid, heptadecanoic acid, stearic acid, oleic acid, vaccenic acid, linoleic acid, arachidic acid, α-linolenic acid, eicosadienoic acid, docosadienoic acid, and 11,14,17-eicosatrienoic acid. However, ARA, DHA, and EPA in the adductor muscle after transplantation were significantly greater than those processed without grafting surgery. These results suggest that pearl oysters require more polyunsaturated FAs (PUFAs) to regulate their inflammatory and immune response after transplantation. However, their ability to biosynthesize unsaturated FAs is limited. Given these results, the addition of PUFA-containing diets or selection of a line with strong ability to biosynthesize unsaturated FAs may be valuable for pearl oyster recovery after transplantation.

The ecdysone receptors and the Nvds in bivalves. a. The ecdysone receptors in mollusk species. b, the expression pattern of Ecr at different development stages in C. gigas. E, egg; TC, two cells; FC, four cells; EM, early morula; M, morula; B, blastula; RM, rotary movement; FS, free swimming;EG, early gastrula stage; G, gastrula; T1, trochophore 1; T2, trochophore 2; T3,trochophore 3; T4, trochophore 4; T5, trochophore 5; ED1, early D-larva 1; ED2, early D-larva 2; D1, D-larva 1; D2, D-larva 2; D3, D-larva 3; D4, D-larva 4; D5, D-larva 5; D6, D-larva 6; D7, D-larva 7; EU1, early umbo larva 1; EU2, early umbo larva 2; U1, umbo larva 1; U2, umbo larva 2; U3, umbo larva 3; U4, umbo larva 4; U5, umbo larva 5; U6, umbo larva 6; LU1, later umbo larva 1; LU2, later umbo larva 2; P1, pediveliger 1; P2, pediveliger 2; S, spat; and J, juvenile. c. the expression pattern of Nvd at different development stages in P. f. martensii and C. gigas. Egg, egg; Fe, fertilized egg; B, blastula; G, gastrula; ET, early trochophore; T, trochophore; D, D-stage larvae; DF, D-stage larvae before feeding; EU, early umbo larvae; EL, eyed larvae; S, spat; J, juveniles. (PDF 772 kb)

Mantle tissue specific genes of P. f. martensii (DOCX 15 kb)

Differentially expressed genes between early trochophore and trochophore stage involved in osteoclast differentiation in P. f. martensii. The red color represented the upregulation at trochophore stage, the green color represented the downregulation at trochophore stage. The yellow color represented the absence genes in P. f. martensii. (PDF 135 kb)

Expression pattern of acetylcholine receptors at different development stage in P. f. martensii. The y-axis is the normalized RPKM value. Egg, egg; Fe, fertilized egg; B, blastula; G, gastrula; ET, early trochophore; T, trochophore; D, D-stage larvae; DF, D-stage larvae before feeding; EU, early umbo larvae; EL, eyed larvae; S, spat; J, juveniles. (PDF 509 kb)

The expression pattern of shell protein coding genes at different development stage in C. gigas. The y-axis is the normalized RPKM value. E, egg; TC, two cells; FC, four cells; EM, early morula; M, morula; B, blastula; RM, rotary movement; FS, free swimming;EG, early gastrula stage; G, gastrula; T1, trochophore 1; T2, trochophore 2; T3,trochophore 3; T4, trochophore 4; T5, trochophore 5; ED1, early D-larva 1; ED2, early D-larva 2; D1, D-larva 1; D2, D-larva 2; D3, D-larva 3; D4, D-larva 4; D5, D-larva 5; D6, D-larva 6; D7, D-larva 7; EU1, early umbo larva 1; EU2, early umbo larva 2; U1, umbo larva 1; U2, umbo larva 2; U3, umbo larva 3; U4, umbo larva 4; U5, umbo larva 5; U6, umbo larva 6; LU1, later umbo larva 1; LU2, later umbo larva 2; P1, pediveliger 1; P2, pediveliger 2; S, spat; and J, juvenile. (PDF 155 kb)

Expression pattern of ECMs in shell matrix at different development stages in C. gigas. The y-axis is the normalized RPKM value. E, egg; TC, two cells; FC, four cells; EM, early morula; M, morula; B, blastula; RM, rotary movement; FS, free swimming;EG, early gastrula stage; G, gastrula; T1, trochophore 1; T2, trochophore 2; T3,trochophore 3; T4, trochophore 4; T5, trochophore 5; ED1, early D-larva 1; ED2, early D-larva 2; D1, D-larva 1; D2, D-larva 2; D3, D-larva 3; D4, D-larva 4; D5, D-larva 5; D6, D-larva 6; D7, D-larva 7; EU1, early umbo larva 1; EU2, early umbo larva 2; U1, umbo larva 1; U2, umbo larva 2; U3, umbo larva 3; U4, umbo larva 4; U5, umbo larva 5; U6, umbo larva 6; LU1, later umbo larva 1; LU2, later umbo larva 2; P1, pediveliger 1; P2, pediveliger 2; S, spat; and J, juvenile. (PDF 243 kb)

Larval development, especially settlement and metamorphosis, has a vital influence on commercial culture during the life cycle of marine invertebrates. Sipunculus nudus, a peanut worm, is an important economic aquaculture species. However, information about the mechanism of its larval settlement and metamorphosis is still limited. Transcriptomic analysis was performed to determine the DEGs between the pelagospheric larva and creeping larva of S. nudus. A total of 96,455 unique unigenes were obtained and 46,355 were annotated. Transcriptome analysis revealed 19,352 DEGs, including 9,923 that were upregulated and 9,429 downregulated after settlement and metamorphosis. KEGG pathway enrichment analyses revealed that these DEGs were mainly involved in the Notch signaling pathway, TNF signaling pathway, protein digestion and absorption, thyroid hormone signaling pathway, and ECM–receptor interaction, and so on. Furthermore, the changes in genes related to cytoskeleton and cell adhesion indicated that protein degradation and apoptosis during metamorphosis mediate the loss of larval cilia and ECM remodeling functions in S. nudus metamorphosis. Changes in genes related to signal transduction and nervous system suggested the cessation of larval swimming, which is involved in settlement and metamorphosis. Changes in genes related to ingestion and digestion indicated that dietary shift occurred with metamorphic transition. Changes in some genes related to stress response and immunity indicated that conditioning induced the immune response of peanut worm. The results improve understanding of the physiological traits controlling S. nudus metamorphosis and provide a solid basis for further study.

Odd-skipped related 1 (OSR1) from Pinctada fucata martensii (PmOSR1) was cloned in this study. PmOSR1 contained an open reading frame measuring 951 bp that encoded a polypeptide of 316 residues. Domain analysis also revealed that PmOSR1 had a typical ZnF_C2H2 domain, indicating high identity with OSR1 protein sequence from Crassostrea gigas (55.25%) and Mizuhopecten yessoensis (65.48%). The expression pattern analysis of PmOSR1 revealed its wide expression in the tissues and developmental stages. PmOSR1 also presented a higher expression in the fast-growing group and hybrid families than in the slow-growing group and inbred families. The polymorphism analysis of PmOSR1 revealed 45 single nucleotide polymorphisms (SNPs) in the genomic sequence, and association analysis presented four SNPs significantly associated with growth traits (namely, shell length, width, height, and shell weight; P